Related papers: A New Class of String Transformations for Compress…
String matching is a fundamental problem in computer science, with critical applications in text retrieval, bioinformatics, and data analysis. Among the numerous solutions that have emerged for this problem in recent decades,…
We study the problem of indexing and compressing tries using a BWT-based approach. Specifically, we consider a succinct and compressed representation of the XBWT of Ferragina et al.\ [FOCS '05, JACM '09] corresponding to the analogous of…
Two decades ago, a breakthrough in indexing string collections made it possible to represent them within their compressed space while at the same time offering indexed search functionalities. As this new technology permeated through…
In this paper, we show that the LZ77 factorization of a text T {\in\Sigma^n} can be computed in O(R log n) bits of working space and O(n log R) time, R being the number of runs in the Burrows-Wheeler transform of T reversed. For extremely…
A new array based data structure named black-white array (BWA) is introduced as an effective and efficient alternative to the list or tree based data structures for dynamic data set. It consists of two sub-arrays, one white and one black of…
High-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to build and store indexes of these databases but constructing such…
Recently, Cenzato et al.\ proposed a new text index, called the \emph{suffixient array}, which is a subset of the suffix array and supports locating a single pattern occurrence or finding its maximal exact matches (MEMs), assuming random…
Recently, Holt and McMillan [Bionformatics 2014, ACM-BCB 2014] have proposed a simple and elegant algorithm to merge the Burrows-Wheeler transforms of a family of strings. In this paper we show that the H&M algorithm can be improved so…
Abbreviations and contractions are commonly found in text across different domains. For example, doctors' notes contain many contractions that can be personalized based on their choices. Existing spelling correction models are not suitable…
A standard format used for storing the output of high-throughput sequencing experiments is the FASTQ format. It comprises three main components: (i) headers, (ii) bases (nucleotide sequences), and (iii) quality scores. FASTQ files are…
While short read aligners, which predominantly use the FM-index, are able to easily index one or a few human genomes, they do not scale well to indexing databases containing thousands of genomes. To understand why, it helps to examine the…
The longest common prefix array is a very advantageous data structure that, combined with the suffix array and the Burrows-Wheeler transform, allows to efficiently compute some combinatorial properties of a string useful in several…
We describe an adaptive context tree weighting (ACTW) algorithm, as an extension to the standard context tree weighting (CTW) algorithm. Unlike the standard CTW algorithm, which weights all observations equally regardless of the depth, ACTW…
In Transformer-based neural machine translation (NMT), the positional encoding mechanism helps the self-attention networks to learn the source representation with order dependency, which makes the Transformer-based NMT achieve…
In this paper we present an algorithm to compute the Lyndon array of a string $T$ of length $n$ as a byproduct of the inversion of the Burrows-Wheeler transform of $T$. Our algorithm runs in linear time using only a stack in addition to the…
Motivated by challenges in pangenomic read alignment, we propose a generalization of Wheeler graphs that we call Wheeler maps. A Wheeler map stores a text $T[1..n]$ and an assignment of tags to the characters of $T$ such that we can…
Variation graphs, which represent genetic variation within a population, are replacing sequences as reference genomes. Path indexes are one of the most important tools for working with variation graphs. They generalize text indexes to…
Despite the recent advancements in offline reinforcement learning via supervised learning (RvS) and the success of the decision transformer (DT) architecture in various domains, DTs have fallen short in several challenging benchmarks. The…
This paper introduces a novel indexing and access method, called Feature- Based Adaptive Tolerance Tree (FATT), using wavelet transform is proposed to organize large image data sets efficiently and to support popular image access mechanisms…
Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs,…